ASSIsT: an automatic SNP scoring tool for in- and outbreeding species

ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called Geno...

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Published inBioinformatics (Oxford, England) Vol. 31; no. 23; pp. 3873 - 3874
Main Authors Di Guardo, Mario, Micheletti, Diego, Bianco, Luca, Koehorst-van Putten, Herma J J, Longhi, Sara, Costa, Fabrizio, Aranzana, Maria J, Velasco, Riccardo, Arús, Pere, Troggio, Michela, van de Weg, Eric W
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.12.2015
Subjects
Alleles
Animals
Applications Notes
Genotyping Techniques - methods
Humans
Laboratorium voor Plantenveredeling
Laboratory of Plant Breeding
PBR Biodiversiteit en Genetische Variatie
PBR Biodiversity and genetic variation
PBR Ornamentals, tissue culture and gene transfer
PBR Siergewassen, Tissue Culture
Plant Breeding
Polymorphism, Single Nucleotide
Software
WUR PB Biodiversiteit en Genetische Variatie
WUR PB Siergewassen, Tissue Culture
Online AccessGet full text

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Abstract ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker-trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux. The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/. eric.vandeweg@wur.nl.
AbstractList ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker-trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux. The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/. eric.vandeweg@wur.nl.
ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio® (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker–trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux. Availability and implementation: The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/ . Contact: eric.vandeweg@wur.nl
UNLABELLEDASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker-trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux.AVAILABILITY AND IMPLEMENTATIONThe software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/.CONTACTeric.vandeweg@wur.nl.
ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio® (GS).ASSIsT builds on GS derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker-trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux.
Abstract ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio® (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker–trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux. Availability and implementation: The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/. Contact:  eric.vandeweg@wur.nl
Author Bianco, Luca
Aranzana, Maria J
Costa, Fabrizio
Troggio, Michela
van de Weg, Eric W
Micheletti, Diego
Koehorst-van Putten, Herma J J
Arús, Pere
Di Guardo, Mario
Longhi, Sara
Velasco, Riccardo
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10.1186/s12864-015-1310-1
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Snippet ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays,...
Abstract ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays,...
UNLABELLEDASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays,...
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SubjectTerms Alleles
Animals
Applications Notes
Genotyping Techniques - methods
Humans
Laboratorium voor Plantenveredeling
Laboratory of Plant Breeding
PBR Biodiversiteit en Genetische Variatie
PBR Biodiversity and genetic variation
PBR Ornamentals, tissue culture and gene transfer
PBR Siergewassen, Tissue Culture
Plant Breeding
Polymorphism, Single Nucleotide
Software
WUR PB Biodiversiteit en Genetische Variatie
WUR PB Siergewassen, Tissue Culture
Title ASSIsT: an automatic SNP scoring tool for in- and outbreeding species
URI https://www.ncbi.nlm.nih.gov/pubmed/26249809
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https://pubmed.ncbi.nlm.nih.gov/PMC4653386
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Volume 31
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